CHELSEA, Mass. – Two years ago, the future looked bleak for Choice Thru Education. After 40 years of offering after-school tutoring, adult and summer education programs for residents of the Bay State’s poorest city, federal bureaucrats cited a computer glitch of their own making to deny the agency’s application for a new round of funding.

Repeated appeals to Washington fell on deaf ears. The denial was based on the U.S. Department of Education refusing to accept the electronic application on its Web site until 46 minutes past its deadline.

In October 2007, an article in the Bay State Banner about the dilemma produced a flurry of calls of sympathy and small contributions, but not enough to stave off imminent closing of the agency.

“Then the day before Christmas, I received a phone call,” said Choice founder Susan S. Clark. “It was the same woman who had called before and left the message, ‘I wanted to tell you: You are not alone.’ This time, she said she was offering a five-year pledge, enough to allow us to stay open until the next federal funding cycle came around.”

The benefactor was Shalin Liu, a Taiwanese philanthropist now living in the Boston area who gives generously to environmental and artistic causes.

Always held together with scotch tape and prayers out of a converted parachute factory in downtown Chelsea, Choice Thru Education has used the donation to keep its doors open and continue running programs that have helped thousands of students and adults learn English, receive tutoring, attend summer education sessions at local universities and get help applying to college.

Another grant from Massport for noise remediation from nearby Logan Airport resulted in the building on Pearl Street getting badly needed new windows.

During a visit to Choice this week, students arriving from Chelsea High sat down with volunteer tutors and staff to review homework. The sounds of young scholars going over math calculations and English essays in a rainbow of accents filled the front room.

Cindi Flores, 18, will graduate from Chelsea High this spring and go on to Suffolk University.

“When I wrote my college essays, I wrote about Choice,” she said. “It really helped me grow as a person and stay focused on the goal of going to college. It also helped me become more involved in the community.”

Karen Samedi, an 18-year-old native of Haiti, will study nursing at Regis College in the fall. “Sue Clark and Choice never let me stop thinking and planning about college,” she said. “They brought me on college visits and practiced interviews. They really helped me out.”

Jafar Hussaini, a 2009 Chelsea High graduate, moved to the U.S. from Kabul, Afghanistan, and will attend American International University in Springfield in September. “If Choice closed down, there would be no opportunity for kids like me to learn English,” he said. “They would be out on the streets.”

Jeanmarie Salvie, now studying health science at the University of Massachusetts Boston, was a homeless teen when she first walked through the doors of Choice Thru Education four years ago. “Sue was there for me every step of the way,” she said. “I was going to give up on myself, but that’s the thing about Choice — they never give up on anyone.”

Choice still faces challenges. Having lost $320,000 in funding under the federal Trio grants that support Upward Bound and other programs, the agency will apply as a new program without the benefit of credits for past experience. U.S. Sen. John F. Kerry, D-Mass., and U.S. Rep. Michael Capuano, D-Mass., have both gone to bat for the agency to work on renewed DOE funding and other sources of assistance. The top DOE officials under the Bush administration have now been replaced with Obama appointees, raising hopes for a more sympathetic hearing.

In the meantime, Clark, who started the agency at the launch of President Johnson’s “War on Poverty,” is preparing for summer sessions at Merrimack College and writing applications for new grants.